translationalEfficiency {ribosomeProfilingQC} | R Documentation

## Translational Efficiency

### Description

Calculate Translational Efficiency (TE). TE is defined as the ratios of the absolute level of ribosome occupancy devided by RNA levels for transcripts.

### Usage

    translationalEfficiency(
      x,
      window,
      RPFsampleOrder,
      mRNAsampleOrder,
      pseudocount = 1,
      log2 = FALSE,
      normByLibSize = FALSE
    )

### Arguments

`x` | Output of getFPKM or normByRUVs. if window is set, it must be output of coverageDepth.
`window` | numeric(1). window size for maximal counts.
`RPFsampleOrder, mRNAsampleOrder` | Sample order of RPFs and mRNAs. The parameters are used to make sure that the order of RPFs and mRNAs in cvgs is corresponding samples.
`pseudocount` | The number will be add to sum of reads count to avoid X/0.
`log2` | Do log2 transform or not.
`normByLibSize` | Normlization by library size or not. If window size is provied and normByLibSize is set to TRUE, the coverage will be normalized by library size.

### Value

A list with RPFs, mRNA levels and TE as a matrix with translational efficiency

### Examples

    ## Not run:
    path <- system.file("extdata", package="ribosomeProfilingQC")
    RPFs <- dir(path, "RPF.*?\\.[12].bam$", full.names=TRUE)
    RNAs <- dir(path, "mRNA.*?\\.[12].bam$", full.names=TRUE)
    gtf <- file.path(path, "Danio_rerio.GRCz10.91.chr1.gtf.gz")
    cnts <- countReads(RPFs, RNAs, gtf, level="gene")
    fpkm <- getFPKM(cnts)
    te <- translationalEfficiency(fpkm)

    ## End(Not run)

[Package ribosomeProfilingQC version 0.99.9 Index]